CellDesigner Tutorial
Friday, April 18th 2008
Laurence Calzone and Andrei Zinovyev
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical
networks.
Download and Install
Download CellDesigner 4.0 beta at http://celldesigner.org.
Choose setup and launch it:
CellDesigner is divided in different frames:
Tree
Drawing
Layer
List
Notes
CellDesigner offers many drawing features:
Compartment
menu
Species
menu
Visualization
Reaction
menu
menu
Boolean logic
menu
Practice
1. Open CellDesigner 4.0 beta
Click on the CellDesigner icon from your desktop.
2. Create a new model
In the menu, choose [File] => [New].
A window opens.
Name the file: test.
Set the dimensions. By default, the dimensions are set to 600 x 400.
Click [OK].
3. Create a reaction
Add two proteins: A and B.
Click in the "Species" menu bar on the protein shape.
A window pops up.
Name the protein A.
Repeat the process and name the second protein B.
Click in the "Reaction" menu bar on state transition.
Go back to the drawing frame and click on protein A.
Several grey squares appear around the protein, choose one of them from which the arrow
will start.
Click on protein B and choose a grey square on which you want the arrow to point.
Click.
4. Add anchor point
A line links two species. The anchor points are the points from which each segment of a line
starts or ends. That way, more freedom is given to the user to place the species where he/she
wants.
Click right on the line where you want to add the anchor point.
Choose [Add Anchor Point].
Repeat the process as many times as needed.
Note: if you choose [To Orthogonal] as opposed to [To Polyline], the segments will
automatically be arranged according to the orthogonal grid. However, the anchor points can
only be added when the mode is Polyline.
5. Add catalysis reaction
Add protein C.
Click on "Catalysis" in the "Reactions" menu bar.
Select protein C on the square of the transition reaction that links A to B.
Click.
6. Set active state
Select protein B.
From the menu [Components], select the option [Set Active].
7. Change color
Right-click on protein C.
Select [Change Color & Shape]
8. Insert compartment
Click on the "Compartment" icon in the drawing menu bar.
Drag the mouse cursor to specify the area of the compartment around our small network.
Name the compartment: Cell.
9. Add residue
Create new model (see 2)
Name it: test2.
Create protein A
Select protein A in [Proteins] Tab
Click [Edit] button
(or right-click on the protein and choose [Edit Protein])
Click on the [add..] button in the [Protein] dialog
Name the residue (tst1).
Click on the [Close] button.
Click on the [Update] button.
Copy & Paste protein “A” and then draw the “State Transition” arrow from “A” to “A”.
Right-click on “A” (right side) and select [Change Identity...].
(or double-click on the protein)
Click on the residue “tst1” in the Dialog window.
Select [phosphorylated] to modify the state of the residue.
Click on the [Apply] button.
10.Change position of the residue
Select protein “A” in [Proteins] Tab (lower panel).
Click [Edit] (you need to click on the protein in the list to be able to edit it).
Click on residue “tst1” in Dialog.
Click [edit...].
Drag [angle] slidebar.
(or you can also click on the residue, hold the mouse and drag the residue where you want)
Update the changes.
11. Create complexes
Create new model (test3).
Create Proteins “A” and “B”.
Copy and Paste both “A” and “B”.
Click on the [Complex] icon and create complex “C”.
Drag Proteins “A” and “B” into complex C.
Draw “Association” arrow.
(you can also use the macro to create a complex).
12. Include genes and RNAs
Create new model (test4)
Create gene, RNA and Protein
Draw “Transcription” and “Translation”
13. Other small reactions
There are other reactions such as degradation or heterodimerization that can be represented as
follows:
14. Add layers
Go to [Edit] and choose [add layer].
A pop-up window appears.
Give name to layer: Layer1.
The Layer menu is clickable.
Add arrows, text, geometric forms to your graph.
Or:
Access the layer functions directly by right-clicking on a species or a reaction.
Choose [Add text].
Name your layer / Write the text you want to see appear on the graph.
15. Connect to databases
The databases
Create a new model and a new Protein, giving a literature name to the Protein
Select the Protein
[Database] →
[Connect to SGD]
[Connect to iHOP]
[Connect to PubMed]
The databases that you can connect to are:
• SGD
• DBGET
• iHOP
• Entrez Gene
• Genome Network Platform
Access the information
Create Proteins “A” and “B”
Draw “State transition” arrow from “A” to “B”
Click on the [Edit Notes] button in the lower right panel to insert information about the
reaction
Click [Edit Notes] or [Edit Protein Notes] buttons to insert information about the reaction or
the selected protein (e.g. PMID: 12345678)
[Database] → [Connect to PubMed] to find articles related to this reaction or to the proteins.
Model databases
You can import curated published models from BioModels.net
16. Layouts
Open a model from the ones available in the samples file of CellDesigner:
[File] → [Open] → samples/MAPK.xml
Define the layout of the model to be orthogonal:
[Layout] → [Orthogonal Layout]
Using the different layouts offered by CellDesigner, you can get these configurations:
Problem
Try to translate this model in CellDesigner (there is not just one single answer).
Guidelines
1. Start by listing the proteins.
2. Determine the different compartments.
3. Think of how many reactions could be hidden in one arrow of this graph.
Our final picture is the result of our understanding of the article and is as follows:
Annexes